View source for 2yfq


==Crystal structure of Glutamate dehydrogenase from Peptoniphilus asaccharolyticus==
<StructureSection load='2yfq' size='340' side='right'caption='[[2yfq]], [[Resolution|resolution]] 2.94&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2yfq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Peptoniphilus_asaccharolyticus Peptoniphilus asaccharolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YFQ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.94&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yfq OCA], [https://pdbe.org/2yfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yfq RCSB], [https://www.ebi.ac.uk/pdbsum/2yfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yfq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DHE2_PEPAS DHE2_PEPAS] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of l-glutamate to alpha-ketoglutarate using NAD(P) as a cofactor. The bacterial enzymes are hexamers and each polypeptide consists of an N-terminal substrate-binding (Domain I) followed by a C-terminal cofactor-binding segment (Domain II). The reaction takes place at the junction of the two domains, which move as rigid bodies and are presumed to narrow the cleft during catalysis. Distinct signature sequences in the nucleotide-binding domain have been linked to NAD vs. NADP specificity, but they are not unambiguous predictors of cofactor preferences. Here, we have determined the crystal structure of NAD-specific Peptoniphilus asaccharolyticus glutamate dehydrogenase in the apo state. The poor quality of native crystals was resolved by derivatization with selenomethionine, and the structure was solved by single-wavelength anomalous diffraction methods. The structure reveals an open catalytic cleft in the absence of substrate and cofactor. Modeling of NAD(+) in Domain II suggests that a hydrophobic pocket and polar residues contribute to nucleotide specificity. Mutagenesis and isothermal titration calorimetry studies of a critical glutamate at the P7 position of the core fingerprint confirms its role in NAD binding. Finally, the cofactor binding site is compared with bacterial and mammalian enzymes to understand how the amino acid sequences and three-dimensional structures may distinguish between NAD vs. NADP recognition.

Crystal structure of NAD-dependent Peptoniphilus asaccharolyticus glutamate dehydrogenase reveals determinants of cofactor specificity.,Oliveira T, Panjikar S, Carrigan JB, Hamza M, Engel PC, Khan AR J Struct Biol. 2011 Oct 31. PMID:22068154<ref>PMID:22068154</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2yfq" style="background-color:#fffaf0;"></div>

==See Also==
*[[Glutamate dehydrogenase 3D structures|Glutamate dehydrogenase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Peptoniphilus asaccharolyticus]]
[[Category: Carrigan JB]]
[[Category: Engel PC]]
[[Category: Hamza M]]
[[Category: Khan AR]]
[[Category: Oliveira T]]
[[Category: Panjikar S]]
[[Category: Sharkey MA]]